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</head><body><div id="loading-box"><div class="loading-left-bg"></div><div class="loading-right-bg"></div><div class="spinner-box"><div class="configure-border-1"><div class="configure-core"></div></div><div class="configure-border-2"><div class="configure-core"></div></div><div class="loading-word">加载中...</div></div></div><div id="sidebar"><div id="menu-mask"></div><div id="sidebar-menus"><div class="author-avatar"><img class="avatar-img" src="https://gitee.com/tanzicai/drawingbed/raw/master/img/20210609205810.png" onerror="onerror=null;src='/img/friend_404.gif'" alt="avatar"/></div><div class="site-data"><div class="data-item is-center"><div class="data-item-link"><a href="/archives/"><div class="headline">文章</div><div class="length-num">35</div></a></div></div><div class="data-item is-center"><div class="data-item-link"><a href="/tags/"><div class="headline">标签</div><div class="length-num">50</div></a></div></div><div class="data-item is-center"><div class="data-item-link"><a 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朋友圈</span></a></div><div class="menus_item"><a class="site-page" href="/link/"><i class="fa-fw fas fa-link"></i><span> 友链</span></a></div><div class="menus_item"><a class="site-page" href="/download/"><i class="fa-fw fas fa--cloud-download"></i><span> 下载</span></a></div><div class="menus_item"><a class="site-page" href="/about/"><i class="fa-fw fas fa-hear"></i><span> 关于</span></a></div></div><div id="toggle-menu"><a class="site-page"><i class="fas fa-bars fa-fw"></i></a></div></div></nav><div id="post-info"><h1 class="post-title">利用R包TCGAbiolinks进行各种数据下载</h1><div id="post-meta"><div class="meta-firstline"><span class="post-meta-date"><i class="far fa-calendar-alt fa-fw post-meta-icon"></i><span class="post-meta-label">发表于</span><time class="post-meta-date-created" datetime="2021-05-07T01:25:00.000Z" title="发表于 2021-05-07 09:25:00">2021-05-07</time><span class="post-meta-separator">|</span><i class="fas fa-history fa-fw post-meta-icon"></i><span class="post-meta-label">更新于</span><time class="post-meta-date-updated" datetime="2021-07-26T15:50:22.000Z" title="更新于 2021-07-26 23:50:22">2021-07-26</time></span><span class="post-meta-categories"><span class="post-meta-separator">|</span><i class="fas fa-inbox fa-fw post-meta-icon"></i><a class="post-meta-categories" href="/categories/%E5%8C%BB%E5%AD%A6%E7%BB%9F%E8%AE%A1/">医学统计</a></span></div><div class="meta-secondline"><span class="post-meta-separator">|</span><span class="post-meta-pv-cv" id="" data-flag-title="利用R包TCGAbiolinks进行各种数据下载"><i class="far fa-eye fa-fw post-meta-icon"></i><span class="post-meta-label">阅读量:</span><span id="busuanzi_value_page_pv"></span></span></div></div></div></header><main class="layout" id="content-inner"><div id="post"><article class="post-content" id="article-container"><p>TCGAbiolinks的优点在于具备一体化的下载整合，无需再使用复杂的方法对下载的单个数据重新进行整合，换句话说，就是TCGAbiolinks包下载的数据是合并了的，不需要整理（TCGAbiolinks数据下载）。<br>TCGAbiolinks的官方网站是：<a target="_blank" rel="noopener" href="http://www.bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html">http://www.bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html</a><br>代码参考：TCGA3.R包TCGAbiolinks下载数据</p>
<h2 id="安装TCGAbiolinks"><a href="#安装TCGAbiolinks" class="headerlink" title="安装TCGAbiolinks"></a>安装TCGAbiolinks</h2><figure class="highlight r"><table><tr><td class="code"><pre><span class="line">&gt; BiocManager::install(<span class="string">&quot;TCGAbiolinks&quot;</span>)</span><br><span class="line">&gt; library(TCGAbiolinks)</span><br></pre></td></tr></table></figure>
<h2 id="选定要下载的cancer类型"><a href="#选定要下载的cancer类型" class="headerlink" title="选定要下载的cancer类型"></a>选定要下载的cancer类型</h2><figure class="highlight r"><table><tr><td class="code"><pre><span class="line">&gt;TCGAbiolinks::getGDCprojects()$project_id</span><br><span class="line"> [<span class="number">1</span>] <span class="string">&quot;TCGA-SARC&quot;</span>             <span class="string">&quot;TARGET-CCSK&quot;</span>          </span><br><span class="line"> [<span class="number">3</span>] <span class="string">&quot;TARGET-NBL&quot;</span>            <span class="string">&quot;TARGET-AML&quot;</span>           </span><br><span class="line"> [<span class="number">5</span>] <span class="string">&quot;TCGA-MESO&quot;</span>             <span class="string">&quot;TCGA-ACC&quot;</span>             </span><br><span class="line"> [<span class="number">7</span>] <span class="string">&quot;TCGA-READ&quot;</span>             <span class="string">&quot;TCGA-LGG&quot;</span>             </span><br><span class="line"> [<span class="number">9</span>] <span class="string">&quot;BEATAML1.0-CRENOLANIB&quot;</span> <span class="string">&quot;TCGA-THCA&quot;</span>            </span><br><span class="line">[<span class="number">11</span>] <span class="string">&quot;VAREPOP-APOLLO&quot;</span>        <span class="string">&quot;HCMI-CMDC&quot;</span>            </span><br><span class="line">[<span class="number">13</span>] <span class="string">&quot;TCGA-CHOL&quot;</span>             <span class="string">&quot;TCGA-KIRC&quot;</span>            </span><br><span class="line">[<span class="number">15</span>] <span class="string">&quot;ORGANOID-PANCREATIC&quot;</span>   <span class="string">&quot;TCGA-BRCA&quot;</span>            </span><br><span class="line">[<span class="number">17</span>] <span class="string">&quot;TCGA-OV&quot;</span>               <span class="string">&quot;TCGA-GBM&quot;</span>             </span><br><span class="line">[<span class="number">19</span>] <span class="string">&quot;TCGA-SKCM&quot;</span>             <span class="string">&quot;GENIE-VICC&quot;</span>           </span><br><span class="line">[<span class="number">21</span>] <span class="string">&quot;TCGA-DLBC&quot;</span>             <span class="string">&quot;CGCI-BLGSP&quot;</span>           </span><br><span class="line">[<span class="number">23</span>] <span class="string">&quot;OHSU-CNL&quot;</span>              <span class="string">&quot;CPTAC-3&quot;</span>              </span><br><span class="line">[<span class="number">25</span>] <span class="string">&quot;BEATAML1.0-COHORT&quot;</span>     <span class="string">&quot;TCGA-KICH&quot;</span>            </span><br><span class="line">[<span class="number">27</span>] <span class="string">&quot;TCGA-UVM&quot;</span>              <span class="string">&quot;TCGA-THYM&quot;</span>            </span><br><span class="line">[<span class="number">29</span>] <span class="string">&quot;TCGA-TGCT&quot;</span>             <span class="string">&quot;TCGA-LUSC&quot;</span>            </span><br><span class="line">[<span class="number">31</span>] <span class="string">&quot;TCGA-PRAD&quot;</span>             <span class="string">&quot;FM-AD&quot;</span>                </span><br><span class="line">[<span class="number">33</span>] <span class="string">&quot;TCGA-UCEC&quot;</span>             <span class="string">&quot;TCGA-LAML&quot;</span>            </span><br><span class="line">[<span class="number">35</span>] <span class="string">&quot;TARGET-ALL-P2&quot;</span>         <span class="string">&quot;TCGA-STAD&quot;</span>            </span><br><span class="line">[<span class="number">37</span>] <span class="string">&quot;TARGET-ALL-P3&quot;</span>         <span class="string">&quot;GENIE-DFCI&quot;</span>           </span><br><span class="line">[<span class="number">39</span>] <span class="string">&quot;GENIE-NKI&quot;</span>             <span class="string">&quot;GENIE-MDA&quot;</span>            </span><br><span class="line">[<span class="number">41</span>] <span class="string">&quot;GENIE-JHU&quot;</span>             <span class="string">&quot;GENIE-MSK&quot;</span>            </span><br><span class="line">[<span class="number">43</span>] <span class="string">&quot;TCGA-ESCA&quot;</span>             <span class="string">&quot;TCGA-HNSC&quot;</span>            </span><br><span class="line">[<span class="number">45</span>] <span class="string">&quot;TARGET-OS&quot;</span>             <span class="string">&quot;TARGET-RT&quot;</span>            </span><br><span class="line">[<span class="number">47</span>] <span class="string">&quot;TCGA-LIHC&quot;</span>             <span class="string">&quot;CTSP-DLBCL1&quot;</span>          </span><br><span class="line">[<span class="number">49</span>] <span class="string">&quot;TCGA-COAD&quot;</span>             <span class="string">&quot;TCGA-LUAD&quot;</span>            </span><br><span class="line">[<span class="number">51</span>] <span class="string">&quot;TCGA-CESC&quot;</span>             <span class="string">&quot;TARGET-WT&quot;</span>            </span><br><span class="line">[<span class="number">53</span>] <span class="string">&quot;NCICCR-DLBCL&quot;</span>          <span class="string">&quot;TCGA-PAAD&quot;</span>            </span><br><span class="line">[<span class="number">55</span>] <span class="string">&quot;MMRF-COMMPASS&quot;</span>         <span class="string">&quot;TARGET-ALL-P1&quot;</span>        </span><br><span class="line">[<span class="number">57</span>] <span class="string">&quot;CPTAC-2&quot;</span>               <span class="string">&quot;TCGA-UCS&quot;</span>             </span><br><span class="line">[<span class="number">59</span>] <span class="string">&quot;TCGA-KIRP&quot;</span>             <span class="string">&quot;TCGA-PCPG&quot;</span>            </span><br><span class="line">[<span class="number">61</span>] <span class="string">&quot;TCGA-BLCA&quot;</span>             <span class="string">&quot;GENIE-UHN&quot;</span>            </span><br><span class="line">[<span class="number">63</span>] <span class="string">&quot;GENIE-GRCC&quot;</span></span><br><span class="line"></span><br></pre></td></tr></table></figure>

<p>选择下载的癌症数据</p>
<figure class="highlight r"><table><tr><td class="code"><pre><span class="line">cancer_type=<span class="string">&quot;TCGA-HNSC&quot;</span></span><br></pre></td></tr></table></figure>

<h2 id="临床数据下载"><a href="#临床数据下载" class="headerlink" title="临床数据下载"></a>临床数据下载</h2><figure class="highlight r"><table><tr><td class="code"><pre><span class="line">clinical &lt;- GDCquery_clinic(project= cancer_type,type = <span class="string">&quot;clinical&quot;</span>)</span><br><span class="line"><span class="comment"># 查看下载的部分数据：</span></span><br><span class="line">clinical[<span class="number">1</span>:<span class="number">4</span>,<span class="number">1</span>:<span class="number">4</span>]</span><br><span class="line">submitter_id year_of_diagnosis classification_of_tumor last_known_disease_status</span><br><span class="line"><span class="number">1</span> TCGA-<span class="number">4</span>P-AA8J              <span class="number">2013</span>            not reported              not reported</span><br><span class="line"><span class="number">2</span> TCGA-BA-<span class="number">4074</span>              <span class="number">2003</span>            not reported              not reported</span><br><span class="line"><span class="number">3</span> TCGA-BA-<span class="number">4075</span>              <span class="number">2004</span>            not reported              not reported</span><br><span class="line"><span class="number">4</span> TCGA-BA-<span class="number">4076</span>              <span class="number">2003</span>            not reported              not reported</span><br><span class="line"><span class="built_in">dim</span>(clinical)</span><br><span class="line">[<span class="number">1</span>] <span class="number">528</span>  <span class="number">78</span> <span class="comment">#是个528行，78列的一个表</span></span><br><span class="line"><span class="comment">#可视化窗口查看数据</span></span><br><span class="line">View(clinical)</span><br></pre></td></tr></table></figure>

<p>可以看出这个表，一行是一个病例，列是根据这个病人的各项信息。</p>
<p><img src="https://gitee.com/tanzicai/drawingbed/raw/master/img/%E4%B8%8B%E8%BD%BD%E6%95%B0%E6%8D%AE%E8%A1%A8%E6%A0%BC%E7%A4%BA%E4%BE%8B.png" alt="img"></p>
<h2 id="实验相关的数据下载"><a href="#实验相关的数据下载" class="headerlink" title="实验相关的数据下载"></a>实验相关的数据下载</h2><p>好说~网上也能搜到各种数据类型的下载方法：</p>
<h3 id="1-RNA-seq的counts数据"><a href="#1-RNA-seq的counts数据" class="headerlink" title="1.RNA-seq的counts数据"></a>1.RNA-seq的counts数据</h3><figure class="highlight r"><table><tr><td class="code"><pre><span class="line">library(dplyr)</span><br><span class="line">library(DT)</span><br><span class="line">library(SummarizedExperiment)</span><br><span class="line">data_type &lt;- <span class="string">&quot;Gene Expression Quantification&quot;</span><span class="comment">#选择数据类型为“基因定量表达”</span></span><br><span class="line">data_category &lt;- <span class="string">&quot;Transcriptome Profiling&quot;</span> <span class="comment">#选择数据类别为转录组</span></span><br><span class="line">workflow_type &lt;- <span class="string">&quot;HTSeq - Counts&quot;</span></span><br><span class="line">query_TranscriptomeCounts &lt;- GDCquery(project = cancer_type, </span><br><span class="line">                                  data.category = data_category, </span><br><span class="line">                                  data.type =  data_type, </span><br><span class="line">                                  workflow.type = workflow_type)</span><br><span class="line"><span class="comment"># GDCquery函数参数详解官网网址：http://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/query.html#useful_information</span></span><br><span class="line"><span class="comment">#然后会弹出一大串下面这些</span></span><br><span class="line">--------------------------------------</span><br><span class="line">o GDCquery: Searching <span class="keyword">in</span> GDC database</span><br><span class="line">--------------------------------------</span><br><span class="line">Genome of reference: hg38</span><br><span class="line">--------------------------------------------</span><br><span class="line">oo Accessing GDC. This might take a while...</span><br><span class="line">--------------------------------------------</span><br><span class="line">ooo Project: TCGA-HNSC</span><br><span class="line">--------------------</span><br><span class="line">oo Filtering results</span><br><span class="line">--------------------</span><br><span class="line">ooo By data.typeooo By workflow.type</span><br><span class="line">----------------</span><br><span class="line">oo Checking data</span><br><span class="line">----------------</span><br><span class="line">ooo Check <span class="keyword">if</span> there are duplicated casesooo Check <span class="keyword">if</span> there results <span class="keyword">for</span> the query</span><br><span class="line">-------------------</span><br><span class="line">o Preparing output</span><br><span class="line">-------------------</span><br><span class="line"><span class="comment">#将上一步搜索得到的数据下载下来，自动存储到所设置目录下的文件夹&gt; GDCdownload(query_TranscriptomeCounts, method = &quot;api&quot;)</span></span><br><span class="line"><span class="comment">#method：使用API (POST方法)或gdc客户端工具。选择“api”,“client”。API更快，但是下载过程中数据可能会损坏，可能需要重新执行。</span></span><br><span class="line">Downloading data <span class="keyword">for</span> project TCGA-HNSCGDC</span><br><span class="line">download will download <span class="number">546</span> files. A total of <span class="number">136.906805</span> MB</span><br><span class="line">Downloading as: Wed_Jan_08_16_55_43_2020.tar.gz</span><br><span class="line">Downloading: <span class="number">140</span> MB</span><br></pre></td></tr></table></figure>

<p>GDCquery函数参数详解官网网址：</p>
<p><a target="_blank" rel="noopener" href="http://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/query.html#useful_information">http://www.bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/query.html#useful_information</a></p>
<figure class="highlight r"><table><tr><td class="code"><pre><span class="line"><span class="comment">#将搜索得到的数据转换为适用于R语言的形式，返回值为a summarizedExperiment or a data.frame---类似矩阵的容器，行名为基因，列名为样本名 </span></span><br><span class="line">&gt; expdat &lt;- GDCprepare(query = query_TranscriptomeCounts) </span><br><span class="line"> </span><br><span class="line">|===================================================================================|<span class="number">100</span>%                     </span><br><span class="line">Completed after 1 m </span><br><span class="line">Starting to add information to samples</span><br><span class="line"> =&gt; Add clinical information to samples</span><br><span class="line">Add FFPE information. More information at: </span><br><span class="line">=&gt; https://cancergenome.nih.gov/cancersselected/biospeccriteria </span><br><span class="line">=&gt; http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html</span><br><span class="line"> =&gt; Adding subtype information to samples</span><br><span class="line">hnsc subtype information from:doi:10.1038/nature14129</span><br><span class="line">Accessing www.ensembl.org to get gene information</span><br><span class="line">Downloading genome information (try:0) Using: Human genes (GRCh38.p13)</span><br><span class="line">From the 60483 genes we couldn&#x27;t map 3971</span><br><span class="line"></span><br><span class="line">#转换</span><br><span class="line">count_matrix=assay(expdat)</span><br><span class="line">#可视化查看矩阵</span><br><span class="line">View(count_matrix)</span><br></pre></td></tr></table></figure>

<p><img src="https://gitee.com/tanzicai/drawingbed/raw/master/img/%E8%BD%AC%E6%8D%A2%E5%90%8E%E7%9F%A9%E9%98%B5.webp" alt="img"></p>
<h3 id="2-下载RNA-seq的FPKM数据"><a href="#2-下载RNA-seq的FPKM数据" class="headerlink" title="2.下载RNA-seq的FPKM数据"></a>2.<strong>下载RNA-seq的FPKM数据</strong></h3><figure class="highlight r"><table><tr><td class="code"><pre><span class="line">&gt; Expr_df &lt;- GDCquery(project = cancer_type,</span><br><span class="line">                     data.category = data_category,</span><br><span class="line">                     data.type =  data_type,</span><br><span class="line">                     workflow.type = <span class="string">&quot;HTSeq - FPKM&quot;</span>)</span><br><span class="line">&gt; GDCdownload(Expr_df, method = <span class="string">&quot;api&quot;</span>, files.per.chunk = <span class="number">100</span>)</span><br><span class="line"><span class="comment">#files.per.chunk：这将使API方法一次只下载n个(files.per.chunk)文件。当数据量过大时，可能会下载出错，可设置files.per.chunk参数减少下载问题。值为整数，即可将文件拆分为几个文件下载，如files.per.chunk = 6。</span></span><br><span class="line">Downloading data <span class="keyword">for</span> project TCGA-HNSC</span><br><span class="line">GDCdownload will download <span class="number">546</span> files. A total of <span class="number">278.868796</span> MB</span><br><span class="line">Downloading chunk <span class="number">1</span> of <span class="number">6</span> (<span class="number">100</span> files, size = <span class="number">51.032322</span> MB) as Wed_Jan_08_19_22_27_2020_0.tar.gz</span><br><span class="line">Downloading: <span class="number">51</span> MB     Downloading chunk <span class="number">2</span> of <span class="number">6</span> (<span class="number">100</span> files, size = <span class="number">51.063004</span> MB) as Wed_Jan_08_19_22_27_2020_1.tar.gz</span><br><span class="line">Downloading: <span class="number">51</span> MB     Downloading chunk <span class="number">3</span> of <span class="number">6</span> (<span class="number">100</span> files, size = <span class="number">51.028334</span> MB) as Wed_Jan_08_19_22_27_2020_2.tar.gz</span><br><span class="line">Downloading: <span class="number">51</span> MB     Downloading chunk <span class="number">4</span> of <span class="number">6</span> (<span class="number">100</span> files, size = <span class="number">51.08847</span> MB) as Wed_Jan_08_19_22_27_2020_3.tar.gz</span><br><span class="line">Downloading: <span class="number">51</span> MB     Downloading chunk <span class="number">5</span> of <span class="number">6</span> (<span class="number">100</span> files, size = <span class="number">51.14113</span> MB) as Wed_Jan_08_19_22_27_2020_4.tar.gz</span><br><span class="line">Downloading: <span class="number">51</span> MB     Downloading chunk <span class="number">6</span> of <span class="number">6</span> (<span class="number">46</span> files, size = <span class="number">23.515536</span> MB) as Wed_Jan_08_19_22_27_2020_5.tar.gz</span><br><span class="line">Downloading: <span class="number">24</span> MB</span><br><span class="line"> </span><br><span class="line">&gt; expdat_2 &lt;- GDCprepare(query = Expr_df)</span><br><span class="line">&gt; Expr_matrix=assay(expdat_2)</span><br><span class="line">&gt; write.csv(Expr_matrix,file = <span class="string">&quot;TCGAbiolinks_HNSC_FPKM.csv&quot;</span>)</span><br></pre></td></tr></table></figure>

<h3 id="3-其他数据下载"><a href="#3-其他数据下载" class="headerlink" title="3. 其他数据下载"></a>3. 其他数据下载</h3><figure class="highlight r"><table><tr><td class="code"><pre><span class="line"><span class="comment">#下载miRNA数据</span></span><br><span class="line">  query &lt;- GDCquery(project = cancer_type, </span><br><span class="line">                    data.category = <span class="string">&quot;Transcriptome Profiling&quot;</span>, </span><br><span class="line">                    data.type = <span class="string">&quot;miRNA Expression Quantification&quot;</span>, </span><br><span class="line">                    workflow.type = <span class="string">&quot;BCGSC miRNA Profiling&quot;</span>)</span><br><span class="line">  </span><br><span class="line">  GDCdownload(query, method = <span class="string">&quot;api&quot;</span>, files.per.chunk = <span class="number">50</span>)</span><br><span class="line">  expdat &lt;- GDCprepare(query = query)</span><br><span class="line">  count_matrix=assay(expdat)</span><br><span class="line">  write.csv(count_matrix,file = paste(cancer_type,<span class="string">&quot;miRNA.csv&quot;</span>,sep = <span class="string">&quot;-&quot;</span>))</span><br><span class="line">  </span><br><span class="line"><span class="comment">#下载Copy Number Variation数据</span></span><br><span class="line">  query &lt;- GDCquery(project = cancer_type, </span><br><span class="line">                    data.category = <span class="string">&quot;Copy Number Variation&quot;</span>, </span><br><span class="line">                    data.type = <span class="string">&quot;Copy Number Segment&quot;</span>)</span><br><span class="line">  </span><br><span class="line">  GDCdownload(query, method = <span class="string">&quot;api&quot;</span>, files.per.chunk = <span class="number">50</span>)</span><br><span class="line">  expdat &lt;- GDCprepare(query = query)</span><br><span class="line">  count_matrix=assay(expdat)</span><br><span class="line">  write.csv(count_matrix,file = paste(cancer_type,<span class="string">&quot;Copy-Number-Variation.csv&quot;</span>,sep = <span class="string">&quot;-&quot;</span>))</span><br><span class="line">  </span><br><span class="line"><span class="comment">#下载甲基化数据</span></span><br><span class="line">  query.met &lt;- GDCquery(project =cancer_type,</span><br><span class="line">                        legacy = <span class="literal">TRUE</span>,</span><br><span class="line">                        data.category = <span class="string">&quot;DNA methylation&quot;</span>)</span><br><span class="line">  GDCdownload(query.met, method = <span class="string">&quot;api&quot;</span>, files.per.chunk = <span class="number">300</span>)</span><br><span class="line">  expdat &lt;- GDCprepare(query = query)</span><br><span class="line">  count_matrix=assay(expdat)</span><br><span class="line">  write.csv(count_matrix,file = paste(cancer_type,<span class="string">&quot;methylation.csv&quot;</span>,sep = <span class="string">&quot;-&quot;</span>))</span><br></pre></td></tr></table></figure>

<h2 id="保存下载表"><a href="#保存下载表" class="headerlink" title="保存下载表"></a>保存下载表</h2><figure class="highlight r"><table><tr><td class="code"><pre><span class="line"><span class="comment">#保存数据</span></span><br><span class="line">save(clinical,file=<span class="string">&quot;BRCA_clinical.Rdata&quot;</span>)</span><br><span class="line"><span class="comment">#导出数据到文件</span></span><br><span class="line">write.csv(clinical, file=<span class="string">&quot;TCGAbiolinks-BRCA-clinical.csv&quot;</span>)</span><br></pre></td></tr></table></figure>



</article><div class="post-copyright"><div class="post-copyright__author"><span class="post-copyright-meta">文章作者: </span><span class="post-copyright-info"><a href="mailto:undefined">谭自财</a></span></div><div class="post-copyright__type"><span class="post-copyright-meta">文章链接: </span><span class="post-copyright-info"><a href="https://tanzicai.gitee.io/2021/05/07/%E5%88%A9%E7%94%A8R%E5%8C%85TCGAbiolinks%E8%BF%9B%E8%A1%8C%E5%90%84%E7%A7%8D%E6%95%B0%E6%8D%AE%E4%B8%8B%E8%BD%BD/">https://tanzicai.gitee.io/2021/05/07/利用R包TCGAbiolinks进行各种数据下载/</a></span></div><div class="post-copyright__notice"><span class="post-copyright-meta">版权声明: </span><span class="post-copyright-info">本博客所有文章除特别声明外，均采用 <a href="https://creativecommons.org/licenses/by-nc-sa/4.0/" target="_blank">CC BY-NC-SA 4.0</a> 许可协议。转载请注明来自 <a href="https://tanzicai.gitee.io" target="_blank">小谭的部落阁</a>！</span></div></div><div class="tag_share"><div class="post-meta__tag-list"><a class="post-meta__tags" href="/tags/TCGA/">TCGA</a><a 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class="card-widget card-announcement"><div class="item-headline"><i class="fas fa-bullhorn card-announcement-animation"></i><span>公告</span></div><div class="announcement_content">本站正在切换主题测试，如有错误提示，请联系我，谢谢</div></div><div class="sticky_layout"><div class="card-widget" id="card-toc"><div class="item-headline"><i class="fas fa-stream"></i><span>目录</span></div><div class="toc-content"><ol class="toc"><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%AE%89%E8%A3%85TCGAbiolinks"><span class="toc-number">1.</span> <span class="toc-text">安装TCGAbiolinks</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E9%80%89%E5%AE%9A%E8%A6%81%E4%B8%8B%E8%BD%BD%E7%9A%84cancer%E7%B1%BB%E5%9E%8B"><span class="toc-number">2.</span> <span class="toc-text">选定要下载的cancer类型</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E4%B8%B4%E5%BA%8A%E6%95%B0%E6%8D%AE%E4%B8%8B%E8%BD%BD"><span class="toc-number">3.</span> <span class="toc-text">临床数据下载</span></a></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E5%AE%9E%E9%AA%8C%E7%9B%B8%E5%85%B3%E7%9A%84%E6%95%B0%E6%8D%AE%E4%B8%8B%E8%BD%BD"><span class="toc-number">4.</span> <span class="toc-text">实验相关的数据下载</span></a><ol class="toc-child"><li class="toc-item toc-level-3"><a class="toc-link" href="#1-RNA-seq%E7%9A%84counts%E6%95%B0%E6%8D%AE"><span class="toc-number">4.1.</span> <span class="toc-text">1.RNA-seq的counts数据</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#2-%E4%B8%8B%E8%BD%BDRNA-seq%E7%9A%84FPKM%E6%95%B0%E6%8D%AE"><span class="toc-number">4.2.</span> <span class="toc-text">2.下载RNA-seq的FPKM数据</span></a></li><li class="toc-item toc-level-3"><a class="toc-link" href="#3-%E5%85%B6%E4%BB%96%E6%95%B0%E6%8D%AE%E4%B8%8B%E8%BD%BD"><span class="toc-number">4.3.</span> <span class="toc-text">3. 其他数据下载</span></a></li></ol></li><li class="toc-item toc-level-2"><a class="toc-link" href="#%E4%BF%9D%E5%AD%98%E4%B8%8B%E8%BD%BD%E8%A1%A8"><span class="toc-number">5.</span> <span class="toc-text">保存下载表</span></a></li></ol></div></div><div class="card-widget card-recent-post"><div class="item-headline"><i class="fas fa-history"></i><span>最新文章</span></div><div class="aside-list"><div class="aside-list-item"><a class="thumbnail" href="/2022/02/10/%E5%B8%B8%E7%94%A8%E7%B1%BB/" title="Java常用类"><img src="https://gitee.com/tanzicai/file-pan/raw/master/img/20220209171157.png" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="Java常用类"/></a><div class="content"><a class="title" href="/2022/02/10/%E5%B8%B8%E7%94%A8%E7%B1%BB/" title="Java常用类">Java常用类</a><time datetime="2022-02-10T12:25:00.000Z" title="发表于 2022-02-10 20:25:00">2022-02-10</time></div></div><div class="aside-list-item"><a class="thumbnail" href="/2022/02/09/%E5%BC%82%E5%B8%B8/" title="Java异常"><img src="/img/survivors_v03_5120x2880.png" onerror="this.onerror=null;this.src='/img/404.jpg'" alt="Java异常"/></a><div 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